What am I supposed to examing my data for? They seem to be correct. Should I just barge on ahead? (I'm OK with the matrix smoothing, I think.)
When I submitted that matrix to fa, I got a result that seems to make sense. But again, loads of warnings. E.g.,
Warning messages:
1: In cor.smooth(R) : Matrix was not positive definite, smoothing was done
2: In cor.smooth(R) : Matrix was not positive definite, smoothing was done
3: In cor.smooth(R) : Matrix was not positive definite, smoothing was done
4: In cor.smooth(r) : Matrix was not positive definite, smoothing was done
5: In fa.stats(r = r, f = f, phi = phi, n.obs = n.obs, np.obs = np.obs, :
The estimated weights for the factor scores are probably incorrect. Try a different factor extraction method.
I thought that the smoothing had already been done!
And what "different factor extraction method" should I consider?
So then I turned to lavaan. I declared my ordered factors in R and used lavCor, which tells me that it knows how to handle ordinal data variables. This gave me:
cor2 <- lavCor(csbx1[-18], missing = 'pairwise', output = 'cor')
Warning message:
In lavaan(slotParTable = PT.un, slotData = lav.data, model.type = "unrestricted", :
lavaan WARNING: estimation of the baseline model failed.
I can't find any documentation about what this warning means. But it was only a warning, so I barged on ahead.
efa1 <- efaUnrotate(csbx1, nf=4, missing = 'pairwise')
efa1 <- efaUnrotate(csbx1, nf=4, missing = 'pairwise')
Warning message:
In lav_object_post_check(object) :
lavaan WARNING: some estimated ov variances are negative [I know that this is impossible, and probably results from some missing data and "pairwise deletion."
efa2 <- oblqRotate(efa1, method = 'quartimin')
> efa2 <- oblqRotate(efa1, method = 'quartimin')
> efa2 ... Sensible result output followed by:
The standard errors are close but do not match with other packages. Be mindful when using it.
Warning message:
In testLoadings(object) :
The standard error is currently invalid because it does not account for the variance of the rotation function. It is simply based on the delta method.
Hardly reassuring.
I know that this is a lavaan support site. I can't find a similar psych support site to ask about the psych issues. Is there one? Are the folks here open to try to help a relative newbie on psych package issues? And lavaan seems to assume that I will know what its warnings mean. Is there some good documentation about the meaning of the lavaan warnings? Can I trust the results I have gotten from either of the psych or lavaan approaches?
I would really appreciate some help with all of the above.
Larry Hunsicker